Prediction Accuracies of Genomic Selection for Nine Commercially Important Traits in the Portuguese Oyster (Crassostrea angulata) Using DArT-Seq Technology

Genomic selection has been widely used in terrestrial animals but has had limited application in aquaculture due to relatively high genotyping costs. Genomic information has an important role in improving the prediction accuracy of breeding values, especially for traits that are difficult or expensive to measure. The purposes of this study were to (i) further evaluate the use of genomic information to improve prediction accuracies of breeding values from, (ii) compare different prediction methods (BayesA, BayesCπ and GBLUP) on prediction accuracies in our field data, and (iii) investigate the effects of different SNP marker densities on prediction accuracies of traits in the Portuguese oyster (Crassostrea angulata). The traits studied are all of economic importance and included morphometric traits (shell length, shell width, shell depth, shell weight), edibility traits (tenderness, taste, moisture content), and disease traits (Polydora sp. and Marteilioides chungmuensis). A total of 18,849 single nucleotide polymorphisms were obtained from genotyping by sequencing and used to estimate genetic parameters (heritability and genetic correlation) and the prediction accuracy of genomic selection for these traits. Multi-locus mixed model analysis indicated high estimates of heritability for edibility traits; 0.44 for moisture content, 0.59 for taste, and 0.72 for tenderness. The morphometric traits, shell length, shell width, shell depth and shell weight had estimated genomic heritabilities ranging from 0.28 to 0.55. The genomic heritabilities were relatively low for the disease related traits: Polydora sp. prevalence (0.11) and M. chungmuensis (0.10). Genomic correlations between whole weight and other morphometric traits were from moderate to high and positive (0.58–0.90). However, unfavourably positive genomic correlations were observed between whole weight and the disease traits (0.35–0.37). The genomic best linear unbiased prediction method (GBLUP) showed slightly higher accuracy for the traits studied (0.240–0.794) compared with both BayesA and BayesCπ methods but these differences were not significant. In addition, there is a large potential for using low-density SNP markers for genomic selection in this population at a number of 3000 SNPs. Therefore, there is the prospect to improve morphometric, edibility and disease related traits using genomic information in this species

Molecular Characterisation of Colour Formation in the Prawn <em>Fenneropenaeus merguiensis</em>

<div><p>Introduction</p><p>Body colouration in animals can have a range of functions, with predator protection an important aspect of colour in crustaceans. Colour determination is associated with the carotenoid astaxanthin, which is taken up through the diet and stabilised in the tissues by the protein crustacyanin. As a variety of genes are found to play a role in colour formation in other systems, a holistic approach was employed in this study to determine the factors involved in <i>Fenneropenaeus merguiensis</i> colouration.</p> <p>Results</p><p>Full length <i>F. merguiensis</i> crustacyanin subunit A and C sequences were isolated. Crustacyanin subunit A and C were found in the <i>F. merguiensis</i> transcriptomes of the muscle/cuticle tissue, hepatopancreas, eye stalk and nervous system, using 454 next generation sequencing technology. Custom microarray analysis of albino, light and dark <i>F. merguiensis</i> cuticle tissue showed genes encoding actin, sarcoplasmic calcium-binding protein and arginine kinase to be 4-fold or greater differentially expressed (<i>p</i><0.05) and down-regulated in albinos when compared to light and dark samples. QPCR expression analysis of crustacyanin and total astaxanthin pigment extraction revealed significantly (<i>p</i><0.05) lower crustacyanin subunit A and C gene transcript copy numbers and total astaxanthin levels in albinos than in the light and dark samples. Additionally, crustacyanin subunit A and C expression levels correlated positively with each other.</p> <p>Conclusions</p><p>This study identified gene products putatively involved in crustacean colouration, such as crustacyanin, sarcoplasmic calcium-binding protein and forms of actin, and investigated differences in gene expression and astaxanthin levels between albino, light and dark coloured prawns. These genes open a path to enhance our understanding of the biology and regulation of colour formation.</p> </div

Example of cooked albino (a), light (b) and dark (c) <i>F. merguiensis</i> used in this study.

<p>Albino (a), light (b) and dark (c) prawns in the top row are uncooked, with a photo of the same animal after cooking directly below for comparison.</p

Primer pairs for qPCR analysis of dark, light and albino <i>F. merguiensis</i> individuals.

<p>Primer pairs for qPCR analysis of dark, light and albino <i>F. merguiensis</i> individuals.</p

Scatter plot of crustacyanin subunit A and total astaxanthin levels.

<p>All colour groups were included into the scatter plot (0 = albino, 1 = light, 2 = dark), with crustacyanin subunit A and C showing the same pattern (subunit C not shown).</p

Degenerative primers used for the isolation of crustacyanin subunit A and C.

*<p><b>N</b> = A, C, T or G; <b>Y</b> = C or T; <b>R</b> = A or G; <b>H</b> = A, C or T; <b>D</b> = A, G or T.</p